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- PDB-3p4o: Crystal Structure of H2-Kb in complex with the mutant NP205-LCMV-... -

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Basic information

Entry
Database: PDB / ID: 3p4o
TitleCrystal Structure of H2-Kb in complex with the mutant NP205-LCMV-V3A epitope YTAKYPNL, an 8-mer modified peptide from the LCMV
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-B alpha chain
  • NP205-LCMV epitope, YTAKYPNL
KeywordsIMMUNE SYSTEM / H2-Kb / LCMV-V3A / LCMV / TCR / T cell / MHC / viral escape
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / RNA-templated viral transcription / negative stranded viral RNA replication / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / helical viral capsid ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / RNA-templated viral transcription / negative stranded viral RNA replication / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / helical viral capsid / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / sensory perception of smell / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / protein refolding / viral nucleocapsid / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / host cell cytoplasm / learning or memory / hydrolase activity / defense response to bacterium / ribonucleoprotein complex / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / RNA binding / metal ion binding / cytosol
Similarity search - Function
Nucleocapsid protein, arenaviridae / Nucleocapsid, N-terminal, Arenaviridae / Nucleocapsid, C-terminal, Arenaviridae / Nucleocapsid, C-terminal superfamily / Arenavirus nucleocapsid N-terminal domain / Arenavirus nucleocapsid C-terminal domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 ...Nucleocapsid protein, arenaviridae / Nucleocapsid, N-terminal, Arenaviridae / Nucleocapsid, C-terminal, Arenaviridae / Nucleocapsid, C-terminal superfamily / Arenavirus nucleocapsid N-terminal domain / Arenavirus nucleocapsid C-terminal domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETYL GROUP / Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain / Nucleoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGras, S. / Guillonneau, C. / Rossjohn, J.
CitationJournal: To be Published
Title: Crystal Structure of H2-Kb in complex with the mutant NP205-LCMV-V3A epitope YTAKYPNL, an 8-mer modified peptide from the LCMV
Authors: Gras, S. / Guillonneau, C. / Rossjohn, J.
History
DepositionOct 6, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
C: NP205-LCMV epitope, YTAKYPNL
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: Beta-2-microglobulin
F: NP205-LCMV epitope, YTAKYPNL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6438
Polymers89,5556
Non-polymers882
Water8,323462
1
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
F: NP205-LCMV epitope, YTAKYPNL


Theoretical massNumber of molelcules
Total (without water)44,7773
Polymers44,7773
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-16 kcal/mol
Surface area19550 Å2
MethodPISA
2
C: NP205-LCMV epitope, YTAKYPNL
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8655
Polymers44,7773
Non-polymers882
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-14 kcal/mol
Surface area19040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.750, 85.050, 89.180
Angle α, β, γ (deg.)90.000, 111.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein H-2 class I histocompatibility antigen, K-B alpha chain / H-2K(B)


Mass: 32102.855 Da / Num. of mol.: 2 / Fragment: Extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K1, H2-K / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01901
#2: Protein Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01887
#3: Protein/peptide NP205-LCMV epitope, YTAKYPNL / Nucleocapsid protein


Mass: 970.100 Da / Num. of mol.: 2 / Mutation: V3A / Source method: obtained synthetically / Details: SYNTHETIC PEPTIDE / References: UniProt: Q91B91
#4: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M ammonium acetate, 16-24% PEG 3350, 0.1M Na-cacodylate, pH 6.5, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. obs: 41372 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 33.447 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 17.87
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.3-2.40.4670.5174.137259491649110.55599.9
2.4-2.50.3680.4115.131693417841750.44199.9
2.5-2.60.2980.3456.226971355135470.37199.9
2.6-2.70.2480.2737.723204306730620.29399.8
2.7-2.80.1970.2278.920092265026440.24499.8
2.8-2.90.1570.17710.917455229022900.189100
2.9-30.1210.14712.915146199519880.15899.6
3-3.50.0710.09119.652435690168960.09899.9
3.5-40.0350.05431.529376389038800.05899.7
4-50.0260.0440.229115386738610.04399.8
5-60.030.04337.212978173617310.04699.7
6-100.0290.03939.313679186218550.04299.6
100.0160.0354.235765415320.03298.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
PHASERphasing
PHENIX1.6.1_357refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vac

1vac


Resolution: 2.3→61.694 Å / Occupancy max: 1 / Occupancy min: 0.47 / SU ML: 0.37 / σ(F): 0.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2746 1873 5.01 %
Rwork0.2016 --
obs0.2053 37392 90.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.663 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso max: 91.51 Å2 / Biso mean: 28.8263 Å2 / Biso min: 8.38 Å2
Baniso -1Baniso -2Baniso -3
1--5.497 Å20 Å21.9604 Å2
2--10.4462 Å20 Å2
3----4.9492 Å2
Refinement stepCycle: LAST / Resolution: 2.3→61.694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6296 0 6 462 6764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076498
X-RAY DIFFRACTIONf_angle_d1.1028818
X-RAY DIFFRACTIONf_chiral_restr0.074904
X-RAY DIFFRACTIONf_plane_restr0.0051149
X-RAY DIFFRACTIONf_dihedral_angle_d15.7532418
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.38230.31741570.25093047320478
2.3823-2.47760.37371590.25213187334681
2.4776-2.59040.30841570.25463269342684
2.5904-2.7270.38051790.24533359353886
2.727-2.89780.32591810.22763518369989
2.8978-3.12160.26932000.2123635383593
3.1216-3.43570.26862240.19563773399796
3.4357-3.93270.22741990.17293870406998
3.9327-4.95450.22442110.14763911412299
4.9545-61.71610.23182060.16473950415698

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